[gmx-users] Simulation single unit of a dimer

[raja]

Dear David,
Thanks for your reply and your suggestion is helping me.

By,
B.Nataraj

On Mon, 06 Nov 2006 09:12:32 +0100, "David van der Spoel"
<spoel at xray.bmc.uu.se> said:
> raja wrote:
> > Dear gmxions,
> > The protein, which I am going to simulate, is a dimer, but my study
> > through MD is not related of dimer interaction but its catalytic
> > activity. So my question is can I simulate a unit of the dimer? Will
> > that system be physically right to simulate? The individual unit of the
> > dimer is performing the same catalytic activity but act individually.
> > Your thought for this question would be very useful for me.
> > 
> > With thanks!
> > B.Nataraj
> It depends, the dimer may give stability that is necessary for 
> catalysis. To be on the safe side use the dimer. It will also give you 
> twice the statistics for your analysis. If you'd use the monomer a 
> referee will ask you whether that is justified as well.
> 
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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-- 
  raja
  raja_28 at fastmail.us

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